Hi @Ambiflux
Its quite difficult to upgrade to newer version if you have made the customizations directly in ERPNext. I don’t know much about this, but you can create a custom app with all the changes and customizations. Then when you update the latest version, you can install it. Its better to create the app on Frappe V13.
Also, it is better to take a backup of the system, do one upgrade at a time (refer below thread).
You may want to first create a clone of your system and proceed on it before upgrading on the actual production instance.